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ReactionMechanismGenerator / RMG-Py Public

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New style adjacency list and multiplicity label#217

Closed

bbuesser wants to merge 52 commits into

ReactionMechanismGenerator:masterReactionMechanismGenerator/RMG-Py:masterfrom

bbuesser:new-style-adjacency-listbbuesser/RMG-Py:new-style-adjacency-listCopy head branch name to clipboard

Conversation Commits52 (52)Checks Files changed

Closed

New style adjacency list and multiplicity label#217
bbuesser wants to merge 52 commits into
ReactionMechanismGenerator:masterfrom
bbuesser:new-style-adjacency-list

Commits

Commits on May 19, 2014

Update RMG example 1,3-hexadiene with multiplicity label
bbuesser
committed
Update RMG example c3h4 with multiplicity label
bbuesser
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Update RMG example ch3no2 with multiplicity label
bbuesser
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Update RMG example diesel with multiplicity label
bbuesser
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Update RMG example e85 with multiplicity label
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Update RMG example liquid_phase with multiplicity label
bbuesser
committed
Update RMG example methylformate with multiplicity label
bbuesser
committed
Update RMG example minimal with multiplicity label
bbuesser
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Update RMG example minimal_sensitivity with multiplicity label
bbuesser
committed
Update RMG example TEOS with multiplicity label
bbuesser
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Add multiplicity label to loadEntry for transport libraries
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Add multiplicity label to loadEntry for thermo libraries and groups
bbuesser
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Add multiplicity label to loadEntry for statmech depository
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Add multiplicity label to class Entry and loadEntry for forbidden
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Add multiplicity label to loadEntry for kinetics depository
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Add multiplicity label to loadEntry for kinetic groups
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Add multiplicity label in loadEntry for kinetic libraries
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Add multiplicity label to group.py
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Add printMultiplicity=True to toAdjacencyList() in
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Add multiplicity label to molecule.py
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Update to- and fromAdjacencyList() for multiplicity in Molecule instead
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Use new molecule.multiplicity attribute in qm.molecule
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Add multiplicity to read input file
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Add copy() to reaction.py to make deep copies of reaction objects
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Add multiplicity attribute to Species.py
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Add species multiplicity model.py
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Update family.py for new species multiplicity and search for spin
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Change toAdjacencyList() to new adjacency list style
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Add multiplicity label to saveEntry() for transport libraries.
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Add multiplicity label to saveEntry() for thermo libraries.
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Add multiplicity label to saveEntry() for forbiddenstructures.py
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Replace strip() with split() to read adjacency lists in kinetics library
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Set printMultiplicity label in toAdjacencyList() explicitely to True
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Define type of maxMultiplicity in fromAdjacencyList()
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Prepare molecule.py for new adjacency list style
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Remove maxMultiplicity argument
bbuesser
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Modify adjlist.py to read and write the new-style adjacency list.
bbuesser
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Updating examples with new adjacency list style
bbuesser
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Updating existing unit tests for new adjacency list style
bbuesser
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Remove maxMultiplicity argument
bbuesser
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Updating existing unit test for new adjacency list style
bbuesser
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Update fromRDKitMol() for the new adjacency list style
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Change treatment of missing lone pair card
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Update existing unit test for new adjacency list style
bbuesser
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Prevent species generation from crashing if molecule is None and add
bbuesser
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Update existing unit tests for the new adjacency list style
bbuesser
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Remove merge conflicts
bbuesser
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Add write multiplicity label to kinetics groups
bbuesser
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Commits on May 20, 2014

Add multiplicity and lone pairs to functions required for pickling
bbuesser
committed
Add additional unit test for handling the new adjacency list styles
bbuesser
committed
Prevent species creation from crashing of molecule is an empty vector
bbuesser
committed
Add multiplicity to species unit test for pickling species
bbuesser
committed

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